Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins.

Raul Urrutia,Gwen Lomberk,Juan Iovanna,Marisa Lin,Jose Luis Neira,Gabriel Velez

doi:10.1007/s00894-014-2357-7

Abstract

NUPR1, a small chromatin protein, plays a critical role in cancer development, progression, and resistance to therapy. Here, using a combination of structural bioinformatics and molecular modeling methods, we report several novel findings that enhance our understanding of the biochemical function of this protein. We find that NUPR1 has been conserved throughout evolution, and over time it has undergone duplications and transpositions to form other transcriptional regulators. Using threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations, we generated structural models for four of these proteins: NUPR1a, NUPR1b, NUPR2, and the NUPR-like domain of GTF2-I. Comparative analyses of these models combined with extensive linear motif identification reveal that these four proteins, though similar in their propensities for folding, differ in size, surface changes, and sites amenable for posttranslational modification. Lastly, taking NUPR1a as the paradigm for this family, we built models of a NUPR–DNA complex. Additional structural comparisons revealed that NUPR1 defines a new family of small-groove-binding proteins that share structural features with, yet are distinct from, helix-loop-helix AT-hook-containing HMG proteins. These models and inferences should lead to a better understanding of the function of this group of chromatin proteins, which play a critical role in the development of human malignant diseases.Electronic supplementary materialThe online version of this article (doi:10.1007/s00894-014-2357-7) contains supplementary material, which is available to authorized users.

Highlights

NUPR1, called p8, is a small nonspecific DNA-binding protein that is induced in response to cell stress stimuli of varying degrees, such as simple culture medium replacement, growth inhibitory signals, starvation, hypoxia, apoptosis inducers, and anticancer drugs [1]
Further primary structure analyses of these proteins involved the use of several bioinformatics algorithms for defining linear motifs, such as hidden Markov model (HMM)-based domain scan analyses using the NUPR1 sequences as a seed to search profile databases in the HMMER software package [16], including PeroxiBase profiles, HAMAP profiles, PROSITE patterns, More profiles, Pfam HMMs, Pfam HMMs, PROSITE patterns, and PROSITE profiles
Note that we found that, throughout evolution, there have been proteins which are related to the human NUPR1 but display distinct differences that are revealed by the relatedness of their overall primary structures

Summary

Introduction

NUPR1, called p8, is a small nonspecific DNA-binding protein that is induced in response to cell stress stimuli of varying degrees, such as simple culture medium replacement, growth inhibitory signals, starvation, hypoxia, apoptosis inducers, and anticancer drugs [1]. Sequence analyses of NUPR1 reveal that this protein contains a canonical bipartite domain of positively charged amino acids typical of nuclear-localization signals (NLS) [3] and an Nterminal Pro/Glu/Ser/Thr-rich region [4], suggesting nuclear localization and regulation by the ubiquitin/proteasome system. This notion agrees with experimental data indicating that NUPR1 is a short-lived inducible protein which undergoes cytoplasmic-to-nuclear translocation for binding to DNA and. Nuclear magnetic resonance and circular dichroism analyses using NUPR1 purified from E. coli expression systems suggest that this protein may not readily assume a stable secondary structure, and that

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Conclusion